披碱草属遗传多样性、P基因组特异重复序列克隆和小麦EST-SSR标记开发
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摘要
本报告分为三部分。
第一部分是披碱草属植物的遗传多样性分析。以中国境内的披碱草属物种为研究材料，采用ISSR和SSR标记技术，比较了ISSR和SSR标记在披碱草属植物研究中的可应用性；研究了Elymus dahuricus complex物种在中国境内的遗传多样性状况；采用SSR标记对披碱草属植物模式种E．sibiricus的遗传多样性分布状况进行了分析。主要结果如下：(1)ISSR和SSR标记在披碱草属物种中标记效率比较研究表明，2种标记均表现出较高多态性，基于两种标记的种间聚类状况与物种的倍性水平和形态学相似程度存在较高一致性。在12个种间ISSR标记表现出更高的标记效率，SSR标记则更适于近亲缘物种分析。两种标记的相关性在12个种间表现为显著，在近亲缘水平表现不显著。(2)利用ISSR和SSR标记分析了中国境内4个E．dahuricus complex物种共39个居群的遗传多样性。结果显示，4个E．dahuricus complex物种间分化程度较低。其中Eexcelsus相对独立；E．dahuricus和E tangutorm之间存在一定程度的分化；E．cylindricus介于E．dahuricus和Etangutorm之间。UPGMA系统聚类具有明显的地域特性。其中，青海省东沿及周边地区可能是E．dahuricus complex物种在中国境内发生显著分化的地理分界线。(3)6个E．sibiricus居群的SSR分析表明，在居群内和居群间均存在较为丰富的SSR位点变异。遗传变异主要存在于居群间，居群内SSR位点以杂和状态出现的极低频率，表明E．sibiricus为较严格白花授粉植物。E．sibiricus主要分布区的40个居群研究表明，居群间分化具有明显的地域特性，其中青藏高原地区为E．sibiricus分化状况较为复杂的地区。
第二部分是P基因组特异重复序列的克隆。以冰草及小麦族其它基因组植物为材料，进行冰草P基因组特异重复序列分离研究，获得的主要结果如下：(1)利用回收特异RAPD片段的方法，分离到一个长578bp的冰草P基因组特异DNA重复序列——OPC08_(578)，与Genbank上注册的序列同源比较表明，该序列是冰草P基因组新的特异重复序列。以OPC08_(578)克隆作探针进行Southern杂交表明，该克隆片段在W、H和F基因组也有分布，在ABD、R、V、E、St、Ns、I、D、A等基因组中则无分布。根据OPC08_(578)序列，设计合成了一对特异引物SC-OPC08。该标记可以用来区别P与ABD、R、V、E、St、W、Ns、D、A、C、S、U、I、M、AG基因组，也可用于小麦——冰草附加系中冰草染色质的检测，PCR扩增结果和Southern杂交结果相吻合。(2)利用回收特异ISSR片段的方法，分离到一个长535bp的冰草P基因组特异DNA重复序列——UBC811_(535)，同源比较表明，该序列是P基因组新的特异重复序列。Southern杂交表明，该克隆片段在P基因组有非常强的分布，而子ABD、F、V、H、Ns、R、St等其它基因组无杂交信号。根据UBC811_(535)序列，设计合成了一对特异引物SC-UBC811，该标记可以用于小麦——冰草附加系中冰草染色质的检测。
第三部分是EST-SSR标记的开发和作图。利用普通小麦EST数据库(GenBank／dbEST)中最新的151695条EST序列(2003．7．14～2004．8．24)进行了微卫星序列的筛选，共发现微卫星序列2038个，占整个EST数据库的1.34％。根据筛选得到的微卫星序列设计并合成了249个引物对。PCR扩增表明，166个引物对在不同小麦品种中显示出稳定清晰的带型，可以作为小麦和相关物种的新的EST-SSR分子标记。将其中的93个引物对、193个位点定位到除4A和4B外的19条特定的染色体。利用RIL群体将43个EST-SSR位点绘制到遗传图谱的11条染色体上。对开发的166个EST-SSR引物对的EST在GenBank数据库进行比对分析，有48条EST序列与35种具有生物功能的核酸或蛋白质有同源性，大部分的同源产物来源于普通小麦和栽培水稻。将其中的23条EST序列、推测编码20种蛋白质的基因定位到14条特定的小麦染色体；将涉及5种推测蛋白质基因的12个位点绘制到遗传图谱的6条染色体上。
This report is composed of three parts.
Part I is Genetic Diversity of Elymus species. Using twelve Elymus species collected from China, the usefulness of ISSR and SSR markers in genetic diversity analysis was compared. The genetic diversity of Elymus dahuricus complex species of China was analysed. The differentiation model and genetic diversity distribution of Elymus sibiricus in China were investigated using SSR markers. The main results were as follows. (1) The comparing of the usefulness of ISSR and SSR markers showed that both type markers appeared high polymorphism, and the results of cluster analysis based on ISSR and SSR markers were coincided highly with ploidy level and morphologic taxonomy. For 12 species, ISSR markers had higher marker utility than that of SSR markers. But SSR markers were fit to related species analysis. The relation of genetic similarity matrix between ISSR and SSR was significant for 12 species, but not significant for related species. (2) The genetic diversity of 39 populations of four E. dahuricus complex species collected in China was studied using ISSR and SSR markers. The results showed that the differentiation among E. dahuricus complex species was lower. E. excelsus was a relative independence specie. There was definite differentiation between E. tangutorum and E. dahuricus. E. cylindricus showed complex relationship with others species. The UPGMA cluster appeared obvious zone character. The east of Qinghai province might be the geographical differentiation boundary of E. dahuricus complex species. (3) The analysis of 6 E. sibiricus populations based on SSRs showed that there were plenty SSR locus variances within population and among populations. The main genetic variance existed among population. In another, there was only low percentage of heterozygotes within population. These showed that E. sibiricus was a kind of self-pollination plant. The study of 40 populations from the main distribution area showed that there was obvious zone character among population differentiation. And Qingzang altiplano was the area of complicated genetic variance.
Part II is Cloning of P-genome Specific Repetitive DNA Sequences. Agropyron Gaertn (P genome) and other genome of Triticum were used to isolate P-genome specific repetitive DNA sequences. The main results were as follows: (1) Using the method of reclaiming the products of RAPD, A specific DNA repetitive sequence of P genome in Agropyron, OPC08_(578), was isolated and cloned. Homologous comparison with the DNA sequences registered in GenBank indicated that it was a new P-genome specific DNA repetitive sequence. Southern hybridization showed that OPC08_(578) had the same distribution in the genome W, H and F. But it has no hybridization signals detected in ABD, R, V, E, St, Ns, I, D and A genomes. A pair of specific primers SC-OPC08 were designed according to the sequence of OPC08_(578). This primer could not only distinguish P genome from genomes ABD, R, V, E, St, W, Ns, D, A, C, S, U, I, M and AG, but also could be used in the detection of chromatin of P genome from Wheat-Agropyron addition lines. The results of PCR amplification were consistent with the results of Southern hybridization. (2) Using the method of reclaiming the products of ISSR. A P-genome specific DNA repetitive sequence in Agropyron, UBC811_(535), was isolated and cloned. Homologous comparition indicated that it is a new P-genome specific DNA repetitive sequence. Southern hybridization showed that UBC811_(535) had strong distribution in the P genome. But it has no hybridization signals detected in F, V, H, Ns, R and St genomes. A pair of specific primers SC-UBC811 was designed according to the sequence of UBC811_(535). This primer could be used in the detection of P chromatin from Wheat-Agropyron addition lines.
Part III is Development and mapping of EST-SSR markers in wheat. A number of 151695 wheat expression sequence tags (ESTs) that originated from GenBank/dbEST from July 14, 2003 to August 24, 2004 were used to search for simple sequence repeats (SSRs) with motif 2-5 bp, and 2038 simple sequence repeats (EST-SSRs), which accounted for 1.34% of EST database, were identified. Based on these SSR sequences, 249 EST-SSR primer pairs and 166 amplified clear bands in various wheat cultivars were designed. These EST-SSR markers can be used as new molecular markers in wheat and related species. Using Chinese Spring nulli-tetrasomic lines, 93 EST-SSR primer pairs and 193 EST-SSR loci were located on 19 wheat chromosomes except for 4A and 4B. Forty-three loci were mapped on 11 chromosomes of the genetic framework previously constructed using recombinant inbred lines. EST sequences (166) corresponding to EST-SSR markers were analyzed by the programs BLASTN and BLASTX to obtain their information of bio-function and express types. After sequence similarity assignment, 48 ESTs have 35 kinds of homologous sequences or proteins. The most homologous sequences or proteins are from wheat and rice. 23 ESTs with coding 20 proteins putatively were located on 14 chromosomes and 5 genes of coding proteins putatively with 12 loci were mapping on 6 chromosomes.
第一部分是披碱草属植物的遗传多样性分析。以中国境内的披碱草属物种为研究材料，采用ISSR和SSR标记技术，比较了ISSR和SSR标记在披碱草属植物研究中的可应用性；研究了Elymus dahuricus complex物种在中国境内的遗传多样性状况；采用SSR标记对披碱草属植物模式种E．sibiricus的遗传多样性分布状况进行了分析。主要结果如下：(1)ISSR和SSR标记在披碱草属物种中标记效率比较研究表明，2种标记均表现出较高多态性，基于两种标记的种间聚类状况与物种的倍性水平和形态学相似程度存在较高一致性。在12个种间ISSR标记表现出更高的标记效率，SSR标记则更适于近亲缘物种分析。两种标记的相关性在12个种间表现为显著，在近亲缘水平表现不显著。(2)利用ISSR和SSR标记分析了中国境内4个E．dahuricus complex物种共39个居群的遗传多样性。结果显示，4个E．dahuricus complex物种间分化程度较低。其中Eexcelsus相对独立；E．dahuricus和E tangutorm之间存在一定程度的分化；E．cylindricus介于E．dahuricus和Etangutorm之间。UPGMA系统聚类具有明显的地域特性。其中，青海省东沿及周边地区可能是E．dahuricus complex物种在中国境内发生显著分化的地理分界线。(3)6个E．sibiricus居群的SSR分析表明，在居群内和居群间均存在较为丰富的SSR位点变异。遗传变异主要存在于居群间，居群内SSR位点以杂和状态出现的极低频率，表明E．sibiricus为较严格白花授粉植物。E．sibiricus主要分布区的40个居群研究表明，居群间分化具有明显的地域特性，其中青藏高原地区为E．sibiricus分化状况较为复杂的地区。
第二部分是P基因组特异重复序列的克隆。以冰草及小麦族其它基因组植物为材料，进行冰草P基因组特异重复序列分离研究，获得的主要结果如下：(1)利用回收特异RAPD片段的方法，分离到一个长578bp的冰草P基因组特异DNA重复序列——OPC08_(578)，与Genbank上注册的序列同源比较表明，该序列是冰草P基因组新的特异重复序列。以OPC08_(578)克隆作探针进行Southern杂交表明，该克隆片段在W、H和F基因组也有分布，在ABD、R、V、E、St、Ns、I、D、A等基因组中则无分布。根据OPC08_(578)序列，设计合成了一对特异引物SC-OPC08。该标记可以用来区别P与ABD、R、V、E、St、W、Ns、D、A、C、S、U、I、M、AG基因组，也可用于小麦——冰草附加系中冰草染色质的检测，PCR扩增结果和Southern杂交结果相吻合。(2)利用回收特异ISSR片段的方法，分离到一个长535bp的冰草P基因组特异DNA重复序列——UBC811_(535)，同源比较表明，该序列是P基因组新的特异重复序列。Southern杂交表明，该克隆片段在P基因组有非常强的分布，而子ABD、F、V、H、Ns、R、St等其它基因组无杂交信号。根据UBC811_(535)序列，设计合成了一对特异引物SC-UBC811，该标记可以用于小麦——冰草附加系中冰草染色质的检测。
第三部分是EST-SSR标记的开发和作图。利用普通小麦EST数据库(GenBank／dbEST)中最新的151695条EST序列(2003．7．14～2004．8．24)进行了微卫星序列的筛选，共发现微卫星序列2038个，占整个EST数据库的1.34％。根据筛选得到的微卫星序列设计并合成了249个引物对。PCR扩增表明，166个引物对在不同小麦品种中显示出稳定清晰的带型，可以作为小麦和相关物种的新的EST-SSR分子标记。将其中的93个引物对、193个位点定位到除4A和4B外的19条特定的染色体。利用RIL群体将43个EST-SSR位点绘制到遗传图谱的11条染色体上。对开发的166个EST-SSR引物对的EST在GenBank数据库进行比对分析，有48条EST序列与35种具有生物功能的核酸或蛋白质有同源性，大部分的同源产物来源于普通小麦和栽培水稻。将其中的23条EST序列、推测编码20种蛋白质的基因定位到14条特定的小麦染色体；将涉及5种推测蛋白质基因的12个位点绘制到遗传图谱的6条染色体上。
This report is composed of three parts.
Part I is Genetic Diversity of Elymus species. Using twelve Elymus species collected from China, the usefulness of ISSR and SSR markers in genetic diversity analysis was compared. The genetic diversity of Elymus dahuricus complex species of China was analysed. The differentiation model and genetic diversity distribution of Elymus sibiricus in China were investigated using SSR markers. The main results were as follows. (1) The comparing of the usefulness of ISSR and SSR markers showed that both type markers appeared high polymorphism, and the results of cluster analysis based on ISSR and SSR markers were coincided highly with ploidy level and morphologic taxonomy. For 12 species, ISSR markers had higher marker utility than that of SSR markers. But SSR markers were fit to related species analysis. The relation of genetic similarity matrix between ISSR and SSR was significant for 12 species, but not significant for related species. (2) The genetic diversity of 39 populations of four E. dahuricus complex species collected in China was studied using ISSR and SSR markers. The results showed that the differentiation among E. dahuricus complex species was lower. E. excelsus was a relative independence specie. There was definite differentiation between E. tangutorum and E. dahuricus. E. cylindricus showed complex relationship with others species. The UPGMA cluster appeared obvious zone character. The east of Qinghai province might be the geographical differentiation boundary of E. dahuricus complex species. (3) The analysis of 6 E. sibiricus populations based on SSRs showed that there were plenty SSR locus variances within population and among populations. The main genetic variance existed among population. In another, there was only low percentage of heterozygotes within population. These showed that E. sibiricus was a kind of self-pollination plant. The study of 40 populations from the main distribution area showed that there was obvious zone character among population differentiation. And Qingzang altiplano was the area of complicated genetic variance.
Part II is Cloning of P-genome Specific Repetitive DNA Sequences. Agropyron Gaertn (P genome) and other genome of Triticum were used to isolate P-genome specific repetitive DNA sequences. The main results were as follows: (1) Using the method of reclaiming the products of RAPD, A specific DNA repetitive sequence of P genome in Agropyron, OPC08_(578), was isolated and cloned. Homologous comparison with the DNA sequences registered in GenBank indicated that it was a new P-genome specific DNA repetitive sequence. Southern hybridization showed that OPC08_(578) had the same distribution in the genome W, H and F. But it has no hybridization signals detected in ABD, R, V, E, St, Ns, I, D and A genomes. A pair of specific primers SC-OPC08 were designed according to the sequence of OPC08_(578). This primer could not only distinguish P genome from genomes ABD, R, V, E, St, W, Ns, D, A, C, S, U, I, M and AG, but also could be used in the detection of chromatin of P genome from Wheat-Agropyron addition lines. The results of PCR amplification were consistent with the results of Southern hybridization. (2) Using the method of reclaiming the products of ISSR. A P-genome specific DNA repetitive sequence in Agropyron, UBC811_(535), was isolated and cloned. Homologous comparition indicated that it is a new P-genome specific DNA repetitive sequence. Southern hybridization showed that UBC811_(535) had strong distribution in the P genome. But it has no hybridization signals detected in F, V, H, Ns, R and St genomes. A pair of specific primers SC-UBC811 was designed according to the sequence of UBC811_(535). This primer could be used in the detection of P chromatin from Wheat-Agropyron addition lines.
Part III is Development and mapping of EST-SSR markers in wheat. A number of 151695 wheat expression sequence tags (ESTs) that originated from GenBank/dbEST from July 14, 2003 to August 24, 2004 were used to search for simple sequence repeats (SSRs) with motif 2-5 bp, and 2038 simple sequence repeats (EST-SSRs), which accounted for 1.34% of EST database, were identified. Based on these SSR sequences, 249 EST-SSR primer pairs and 166 amplified clear bands in various wheat cultivars were designed. These EST-SSR markers can be used as new molecular markers in wheat and related species. Using Chinese Spring nulli-tetrasomic lines, 93 EST-SSR primer pairs and 193 EST-SSR loci were located on 19 wheat chromosomes except for 4A and 4B. Forty-three loci were mapped on 11 chromosomes of the genetic framework previously constructed using recombinant inbred lines. EST sequences (166) corresponding to EST-SSR markers were analyzed by the programs BLASTN and BLASTX to obtain their information of bio-function and express types. After sequence similarity assignment, 48 ESTs have 35 kinds of homologous sequences or proteins. The most homologous sequences or proteins are from wheat and rice. 23 ESTs with coding 20 proteins putatively were located on 14 chromosomes and 5 genes of coding proteins putatively with 12 loci were mapping on 6 chromosomes.
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